Re: [gmx-users] mdrun error message in Computing Cluster
Hi, I've never seen that error. I hope you have a compelling scientific reason for installing such a slow old version :-) Mark On Oct 31, 2014 1:58 AM, Agnivo Gosai agnivogromac...@gmail.com wrote: Dear Users I compiled double precision Gromacs 4.5.6 in my university cluster ( named CyEnce ). It is the serial version as I did not compile mdrun separately as parallel mdrun. I followed the procedure in the below mentioned link :- http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Cluster But while using mdrun I am getting the following error :- Reading file em.tpr, VERSION 4.5.6 (double precision) Starting 16 threads tMPI Fatal error in pthreads.c, line 202: Failed to create POSIX thread:Resource temporarily unavailable, rc=11 Aborted I am not sure as to what this means. Any suggestions please ?? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun error message in Computing Cluster
Dear Users I compiled double precision Gromacs 4.5.6 in my university cluster ( named CyEnce ). It is the serial version as I did not compile mdrun separately as parallel mdrun. I followed the procedure in the below mentioned link :- http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Cluster But while using mdrun I am getting the following error :- Reading file em.tpr, VERSION 4.5.6 (double precision) Starting 16 threads tMPI Fatal error in pthreads.c, line 202: Failed to create POSIX thread:Resource temporarily unavailable, rc=11 Aborted I am not sure as to what this means. Any suggestions please ?? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MDRUN error message
On 7/10/14, 12:15 AM, Andy Chao wrote: Dear GROMACS Users: I used the grompp command to run energy minimization of an ionic liquid structure according to the following command: grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr and then run molecular dynamics simulation as the following: mdrun -s NPT.tpr -o NPT.trr when I opend the NPT.trr file, there is nothing inside. Can you explain what was wrong? The last part of the md.log file shows Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size: 3836 Pinning threads with an auto-selected logical core stride of 1 Initializing LinNear Constraints Solver Looks like the run never started. Do other simulations proceed? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
